LECs

Expression of CIITA genes is shown for LEC subsets.

Ciita


Cd80


Cd86


Cd40


Cd70


DCs

Expression of CIITA genes is shown for DC subsets

Ciita


Cd80


Cd86


Cd40


Cd70


Session info

## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
##  [3] LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8       
##  [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
##  [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
##  [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
## [11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8
## 
## time zone: America/Denver
## tzcode source: system (glibc)
## 
## attached base packages:
##  [1] stats4    tools     grid      stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] cli_3.6.1             ggtree_3.8.2          GOSemSim_2.26.1      
##  [4] org.Mm.eg.db_3.17.0   AnnotationDbi_1.62.2  IRanges_2.34.1       
##  [7] S4Vectors_0.38.2      Biobase_2.60.0        BiocGenerics_0.46.0  
## [10] msigdbr_7.5.1         enrichplot_1.20.3     clusterProfiler_4.8.3
## [13] caret_6.0-94          lattice_0.21-8        furrr_0.3.1          
## [16] future_1.33.0         ranger_0.15.1         rsample_1.2.0        
## [19] harmony_1.1.0         biomaRt_2.56.1        openxlsx_4.2.5.2     
## [22] MetBrewer_0.2.0       ggtext_0.1.2          ggtrace_0.2.0.9000   
## [25] qs_0.25.5             vroom_1.6.4           M3Drop_1.26.0        
## [28] numDeriv_2016.8-1.1   djvdj_0.1.0           gtools_3.9.4         
## [31] clustifyrdata_1.1.0   here_1.0.1            presto_1.0.0         
## [34] data.table_1.14.8     Rcpp_1.0.11           devtools_2.4.5       
## [37] usethis_2.2.2         ComplexHeatmap_2.16.0 patchwork_1.1.3      
## [40] scales_1.2.1          boot_1.3-28.1         clustifyr_1.12.0     
## [43] mixtools_2.0.0        broom_1.0.5           colorblindr_0.1.0    
## [46] colorspace_2.1-0      xlsx_0.6.5            RColorBrewer_1.1-3   
## [49] ggrepel_0.9.3         cowplot_1.1.1         knitr_1.44           
## [52] gprofiler2_0.2.2      SeuratObject_4.1.4    Seurat_4.4.0         
## [55] ggforce_0.4.1         ggbeeswarm_0.7.2      lubridate_1.9.3      
## [58] forcats_1.0.0         stringr_1.5.0         dplyr_1.1.3          
## [61] purrr_1.0.2           readr_2.1.4           tidyr_1.3.0          
## [64] tibble_3.2.1          ggplot2_3.4.4         tidyverse_2.0.0      
## 
## loaded via a namespace (and not attached):
##   [1] igraph_1.5.1                ica_1.0-3                  
##   [3] plotly_4.10.2               Formula_1.2-5              
##   [5] zlibbioc_1.46.0             tidyselect_1.2.0           
##   [7] bit_4.0.5                   doParallel_1.0.17          
##   [9] clue_0.3-65                 rjson_0.2.21               
##  [11] blob_1.2.4                  urlchecker_1.0.1           
##  [13] S4Arrays_1.0.6              parallel_4.3.1             
##  [15] png_0.1-8                   ggplotify_0.1.2            
##  [17] goftest_1.2-3               kernlab_0.9-32             
##  [19] densEstBayes_1.0-2.2        uwot_0.1.16                
##  [21] shadowtext_0.1.2            curl_5.1.0                 
##  [23] mime_0.12                   evaluate_0.22              
##  [25] tidytree_0.4.5              leiden_0.4.3               
##  [27] stringi_1.7.12              pROC_1.18.5                
##  [29] backports_1.4.1             XML_3.99-0.14              
##  [31] httpuv_1.6.11               magrittr_2.0.3             
##  [33] rappdirs_0.3.3              splines_4.3.1              
##  [35] prodlim_2023.08.28          RApiSerialize_0.1.2        
##  [37] ggraph_2.1.0                sctransform_0.4.0          
##  [39] sessioninfo_1.2.2           DBI_1.1.3                  
##  [41] jquerylib_0.1.4             withr_2.5.1                
##  [43] class_7.3-22                rprojroot_2.0.3            
##  [45] lmtest_0.9-40               bdsmatrix_1.3-6            
##  [47] tidygraph_1.2.3             htmlwidgets_1.6.2          
##  [49] fs_1.6.3                    SingleCellExperiment_1.22.0
##  [51] segmented_1.6-4             labeling_0.4.3             
##  [53] MatrixGenerics_1.12.3       reticulate_1.32.0          
##  [55] zoo_1.8-12                  XVector_0.40.0             
##  [57] timechange_0.2.0            foreach_1.5.2              
##  [59] fansi_1.0.5                 caTools_1.18.2             
##  [61] timeDate_4022.108           irlba_2.3.5.1              
##  [63] gridGraphics_0.5-1          ellipsis_0.3.2             
##  [65] lazyeval_0.2.2              yaml_2.3.7                 
##  [67] survival_3.5-5              scattermore_1.2            
##  [69] crayon_1.5.2                RcppAnnoy_0.0.21           
##  [71] progressr_0.14.0            tweenr_2.0.2               
##  [73] later_1.3.1                 ggridges_0.5.4             
##  [75] codetools_0.2-19            base64enc_0.1-3            
##  [77] GlobalOptions_0.1.2         profvis_0.3.8              
##  [79] KEGGREST_1.40.1             bbmle_1.0.25               
##  [81] Rtsne_0.16                  shape_1.4.6                
##  [83] filelock_1.0.2              foreign_0.8-84             
##  [85] pkgconfig_2.0.3             xml2_1.3.5                 
##  [87] GenomicRanges_1.52.1        aplot_0.2.2                
##  [89] spatstat.sparse_3.0-2       ape_5.7-1                  
##  [91] viridisLite_0.4.2           xtable_1.8-4               
##  [93] plyr_1.8.9                  httr_1.4.7                 
##  [95] globals_0.16.2              hardhat_1.3.0              
##  [97] pkgbuild_1.4.2              beeswarm_0.4.0             
##  [99] htmlTable_2.4.2             checkmate_2.3.0            
## [101] nlme_3.1-162                loo_2.6.0                  
## [103] HDO.db_0.99.1               dbplyr_2.3.4               
## [105] digest_0.6.33               Matrix_1.6-1.1             
## [107] farver_2.1.1                tzdb_0.4.0                 
## [109] reshape2_1.4.4              ModelMetrics_1.2.2.2       
## [111] yulab.utils_0.1.0           viridis_0.6.4              
## [113] rpart_4.1.19                glue_1.6.2                 
## [115] cachem_1.0.8                BiocFileCache_2.8.0        
## [117] polyclip_1.10-6             Hmisc_5.1-1                
## [119] generics_0.1.3              Biostrings_2.68.1          
## [121] mvtnorm_1.2-3               parallelly_1.36.0          
## [123] pkgload_1.3.3               statmod_1.5.0              
## [125] pbapply_1.7-2               SummarizedExperiment_1.30.2
## [127] gson_0.1.0                  utf8_1.2.3                 
## [129] gower_1.0.1                 graphlayouts_1.0.2         
## [131] StanHeaders_2.26.28         gridExtra_2.3              
## [133] shiny_1.7.5                 lava_1.7.3                 
## [135] GenomeInfoDbData_1.2.10     RCurl_1.98-1.12            
## [137] memoise_2.0.1               rmarkdown_2.25             
## [139] downloader_0.4              RANN_2.6.1                 
## [141] stringfish_0.15.8           spatstat.data_3.0-1        
## [143] rstudioapi_0.15.0           cluster_2.1.4              
## [145] QuickJSR_1.0.7              rstantools_2.3.1.1         
## [147] spatstat.utils_3.0-3        hms_1.1.3                  
## [149] fitdistrplus_1.1-11         munsell_0.5.0              
## [151] rlang_1.1.1                 GenomeInfoDb_1.36.4        
## [153] ipred_0.9-14                circlize_0.4.15            
## [155] mgcv_1.8-42                 xfun_0.40                  
## [157] remotes_2.4.2.1             recipes_1.0.8              
## [159] iterators_1.0.14            matrixStats_1.0.0          
## [161] reldist_1.7-2               abind_1.4-5                
## [163] rstan_2.32.3                treeio_1.24.3              
## [165] rJava_1.0-6                 bitops_1.0-7               
## [167] ps_1.7.5                    promises_1.2.1             
## [169] inline_0.3.19               scatterpie_0.2.1           
## [171] RSQLite_2.3.1               qvalue_2.32.0              
## [173] fgsea_1.26.0                DelayedArray_0.26.7        
## [175] GO.db_3.17.0                compiler_4.3.1             
## [177] prettyunits_1.2.0           listenv_0.9.0              
## [179] tensor_1.5                  MASS_7.3-60                
## [181] progress_1.2.2              BiocParallel_1.34.2        
## [183] gridtext_0.1.5              babelgene_22.9             
## [185] spatstat.random_3.1-6       R6_2.5.1                   
## [187] fastmap_1.1.1               fastmatch_1.1-4            
## [189] vipor_0.4.5                 ROCR_1.0-11                
## [191] nnet_7.3-19                 gtable_0.3.4               
## [193] KernSmooth_2.23-21          miniUI_0.1.1.1             
## [195] deldir_1.0-9                htmltools_0.5.6.1          
## [197] RcppParallel_5.1.7          bit64_4.0.5                
## [199] spatstat.explore_3.2-3      lifecycle_1.0.3            
## [201] zip_2.3.0                   processx_3.8.2             
## [203] callr_3.7.3                 xlsxjars_0.6.1             
## [205] sass_0.4.7                  vctrs_0.6.3                
## [207] spatstat.geom_3.2-5         DOSE_3.26.2                
## [209] ggfun_0.1.3                 sp_2.1-0                   
## [211] future.apply_1.11.0         entropy_1.3.1              
## [213] bslib_0.5.1                 pillar_1.9.0               
## [215] gplots_3.1.3                jsonlite_1.8.7             
## [217] GetoptLong_1.0.5